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981.
Protein structure alignment algorithms play an important role in the studies of protein structure and function. In this paper,
a novel approach for structure alignment is presented. Specifically, core regions in two protein structures are first aligned
by identifying connected components in a network of neighboring geometrically compatible aligned fragment pairs. The initial
alignments then are refined through a multi-objective optimization method. The algorithm can produce both sequential and non-sequential
alignments. We show the superior performance of the proposed algorithm by the computational experiments on several benchmark
datasets and the comparisons with the well-known structure alignment algorithms such as DALI, CE and MATT. The proposed method
can obtain accurate and biologically significant alignment results for the case with occurrence of internal repeats or indels,
identify the circular permutations, and reveal conserved functional sites. A ranking criterion of our algorithm for fold similarity
is presented and found to be comparable or superior to the Z-score of CE in most cases from the numerical experiments. The software and supplementary data of computational results are
available at . 相似文献
982.
Yong Zhang Hongwei Tan Guangju Chen Zongchao Jia 《Journal of molecular recognition : JMR》2010,23(4):360-368
We have studied the conformational transition of the calmodulin binding domains (CBD) in several calmodulin‐binding kinases, in which CBD changes from the disordered state to the ordered state when binding with calmodulin (CaM). Targeted molecular dynamics simulation was used to investigate the binding process of CaM and CBD of CaM‐dependent kinase I (CaMKI–CBD). The results show that CaMKI–CBD began to form an α‐helix and the interaction free energy between CaM and CaMKI–CBD increased once CaM fully encompassed CaMKI–CBD. Two series of CaM/CBD complex systems, including the complexes of CaM with the initially disordered and the final ordered CBD, were constructed to study the interaction using molecular dynamics simulations. Our analyses suggest that the VDW interaction plays a dominant role in CaM/CBD binding and is a key factor in the disorder–order transition of CBD. Additionally, the entropy effect is not in favor of the formation of the CaM/CBD complex, which is consistent with the experimental evidence. Based on the results, it appears that the CBD conformational change from a non‐compact extended structure to compact α‐helix is critical in gaining a favorable VDW interaction and interaction free energy. Copyright © 2009 John Wiley & Sons, Ltd. 相似文献
983.
Ki Yong Lee Young Woong Cho Junghyun Park Dong Young Lee Seung Hyun Kim Young Choong Kim Sang Hyun Sung 《Phytochemical analysis : PCA》2010,21(4):314-321
Introduction – Pulsatilla koreana Nakai, with triterpenoidal saponins as its main pharmacological effective compounds, is known to have several biological activities, including hypoglycaemic, antitumour, cognition‐enhancing, neuroprotective, cytotoxic and antiangiogenic activities. However, few analytical methods have been reported on the quality assessment of P. koreana roots. Obejective – To establish a high‐performance liquid chromatography coupled with evaporative light scattering detection for the simultaneous determination of five triterpenoidal saponins, including pulsatilloside E (1), pulsatilla saponin H (2), anemoside B4 (3), hederacolchiside E (4) and cussosaponin C (5) in P. koreana. Methodology – The chromatographic separation was performed on a Shiseido CapCell PAK C18 analytical column efficiently using gradient elution with acetonitrile and water. Results – All calibration curves showed excellent linear regressions (R2 > 0.9996) within the range of tested concentrations. The intra‐ and inter‐day variations were below 4.78% in terms of RSD. The recoveries were 94.82–102.97% with RSD of 0.27–3.92% for spiked P. koreana samples. Conclusion – The validated method was successfully used for the analysis of five saponins in P. koreana from different locations. Moreover, the different samples were clustered in accordance with contents of triterpenoidal saponins based on aglycon type by a principal component analysis. Copyright © 2010 John Wiley & Sons, Ltd. 相似文献
984.
Kap‐Hoon Han Yoon‐Hee Chun Bárbara De Castro Pimentel Figueiredo Frederico Marianetti Soriani Marcela Savoldi Agostinho Almeida Fernando Rodrigues Charlie Timothy Cairns Elaine Bignell Jaqueline Moisés Tobal Maria Helena S. Goldman Jong‐Hwan Kim Yong‐Sun Bahn Gustavo Henrique Goldman Márcia Eliana Da Silva Ferreira 《Molecular microbiology》2010,75(6):1372-1388
Carbon dioxide (CO2) and its hydration product bicarbonate (HCO3‐) are essential molecules in various physiological processes of all living organisms. The reversible interconversion between CO2 and HCO3‐ is in equilibrium. This reaction is slow without catalyst, but can be rapidly facilitated by Zn2+‐metalloenzymes named carbonic anhydrases (CAs). To gain an insight into the function of multiple clades of fungal CA, we chose to investigate the filamentous fungi Aspergillus fumigatus and A. nidulans. We identified four and two CAs in A. fumigatus and A. nidulans, respectively, named cafA‐D and canA‐B. The cafA and cafB genes are constitutively, strongly expressed whereas cafC and cafD genes are weakly expressed but CO2‐inducible. Heterologous expression of the A. fumigatus cafB, and A. nidulans canA and canB genes completely rescued the high CO2‐requiring phenotype of a Saccharomyces cerevisiaeΔnce103 mutant. Only the ΔcafAΔcafB and ΔcanB deletion mutants were unable to grow at 0.033% CO2, of which growth defects can be restored by high CO2. Defects in the CAs can affect Aspergilli conidiation. Furthermore, A. fumigatusΔcafA, ΔcafB, ΔcafC, ΔcafD and ΔcafAΔcafB mutant strains are fully virulent in a low‐dose murine infection. 相似文献
985.
986.
Yong Wang Hong Lu Qiang Zhu Shibo Jiang Yun Liao 《Bioorganic & medicinal chemistry letters》2010,20(1):189-192
A new series of N-carboxyphenylpyrrole ligands were designed using GeometryFit based on an X-ray crystal structure of gp41. The synthesized ligands showed significant inhibitory activities against HIV gp41 6-helix bundle formation, HIV-1 mediated cell–cell fusion and HIV-1 replication. 相似文献
987.
Nguyen Huu Tung Gyu Yong Song Jeong-Ah Kim Jae-Hee Hyun Hee-Kyoung Kang Young Ho Kim 《Bioorganic & medicinal chemistry letters》2010,20(1):309-314
Six dammarane-type saponins, including three new compounds, floralginsenosides Ta–Tc (1–3), and three known, floralginsenoside Td (4), ginsenoside F1 (5), and ginsenoside F5 (6), were isolated from the flower buds of Panax ginseng. Floralginsenoside Td (4) was first isolated from natural plant sources. Their structures were elucidated on the basis of extensive chemical and spectroscopic methods. Compounds 1, 5, and 6 showed cytotoxic activities towards the HL-60 human leukemia cell line with respective IC50 values of 36.3, 23.2, and 62.4 μM. In addition, after the HL-60 cells were treated with these compounds, several apoptosis events, including chromatin condensation and increase in the population of sub-G1 hypodiploid cells, were observed. 相似文献
988.
Jehun Choi Sung Jin Bae Young Mi Ha Jae Kyung No Eun Kyeong Lee Jun Sik Lee Suhee Song Hyojin Lee Hongsuk Suh Byung Pal Yu Hae Young Chung 《Bioorganic & medicinal chemistry letters》2010,20(16):4882-4884
In searching for new agents with a depigmenting effect, we synthesized a derivative of resveratrol, 5-(6-hydroxy-2-naphthyl)-1,2,3-benzenetriol (5HNB) with a potent tyrosinase inhibitory activity. 5HNB inhibited mushroom tyrosinase with an IC50 value of 2.95 μM, which is more potent than the well-known anti-tyrosinase activity of kojic acid (IC50 = 38.24). The results of the enzymatic inhibition kinetics by Lineweaver–Burk analysis indicated 5HNB inhibits tyrosinase non-competitively when l-tyrosine was used as the substrate. Based on the strong inhibitory action of 5HNB, it is expected that 5HNB can suppress melanin production in which tyrosinase plays the essential role. Our expectation was confirmed by the experimentations with B16 melanoma cells in which 5HNB inhibited melanin production. We propose that 5HNB might have skin-whitening effects as well as therapeutic potential for treating skin pigmentation disorders. 相似文献
989.
990.